Journal club – Protein Space. Big, isn’t it?

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Simplistic combinatorial analyses are an honoured tradition in anti-evolutionary circles. Hoyle’s is the archetype of the combinatorial approach, and he gets a whole fallacy named after him for his trouble. The approach will be familiar – a string of length n composed of v different kinds of subunit is one point in a permutation space containing vn points in total. The chance of hitting any given sequence in one step, such as the one you have selected as ‘target’, is the reciprocal of that number. Exponentiation being the powerful tool it is, it takes only a little work with a calculator to assess the permutations available to the biological polymers DNA and protein and come up with some implausibly large numbers and conclude that Life – and, if you are feeling bold, evolution – is impossible.

Dryden, Thomson and White of Edinburgh University’s Chemistry department argue in this 2008 paper that not only is the combinatorial space of the canonical 20 L-acids much smaller than simplistically assumed, but more surprisingly, that it is sufficiently small to have been explored completely during the history of life on earth. Continue reading

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One question you’d like to ask God

Many people, including the religious, have questions they would like to ask God. Let’s see which ones are the most popular.

One question you’d like to ask God
  • Add your answer
© Kama

Do you have a question you’d like to ask God that is not mentioned in the poll? Write it in the comments section.

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Is anything in biology , man, beast, plant, in millions etc of species evolving as we speak?

I say no but why do evolutionists?

This is a sly way to demonstrate how unlikely evolutionism is on a probability curve.when on thinks of the millions (billions?) of segregated populations in biology(species) then it should be a high, or respectable percentage, are evolving as we speak to create new populations with new bodyplans to survive in some niche. By high I mean millions, with a allowance for mere hundreds of thousands. YET I am confident there is none evolving today. further i suspect evolutionists would say there is none evolving today. WHY? If not today what about yesterday or 300 years ago? Why couldn’t creationists say its not happening today because it never happened? Its accurate sampling of todays non evolution for predicting none in the past!

i think the only hope (hope?) is if evolutionism said , under pE influence, that all biology today is in the stasis stage and just waiting for a sudden need to change, qickly done, then stasis again. Yet why would it be that stasis has been reached so perfectly today relative to the enormous claim of the need in the past for evolutionism?

Anyways i think creationists have a good point here but willing to be corrected.

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15.5 hours.

Over two working days.

In this comment colewd says: “Let’s start with this overview.”

An “overview” that according to this tool contains 187153 words.

Where those words according to this tool will take over 15 hours to read.

15 hours for an “overview”. 15 hours.

If only there was some way to take a sprawling set of claims and refine them down into a core that could then be reviewed by others and feedback given until it is a reasonable size (typically 3,000 to 10,000 words on the average scientific paper) where all claims have been tested by other experts and errors removed.

It seems to be it’s a strategy. Never get pinned down on anything too specific and you never have to be wrong. Hence the sprawl.

colewd, do you seriously expect people to spend 15 hours reading an “overview”? How long is the main argument? A million or two words?

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’Divergence of Character’ Myth

As shown repeatedly, “Nothing in Evolution Makes Sense. Period.” Not natural selection, gradualism, human evolution, UCD, tree of life, etc. And just to confirm, let’s look at another one of the nonsensical concepts of “evolution”.

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Does Swamidass’ new “genealogical adams and eves” hypothesis unknowingly serve to “make God a monster”?

As 2020 both cools down in temperature and heats up in rhetoric, here is a response to S. Joshua Swamidass’ recent book that deserves more air time given how a few evangelical Protestant theologians and apologists are expressing surprised praise at it, calling it a ‘game changer’ because of ‘genealogy’ vs. ‘genetics’. I would consider it a ‘game changer’ only in a borrowed or catch-up sense of that term, given Swamidass’ YECist+ audience. Any thoughts here on this critical review of the book by a fellow evangelical active at BioLogos?

From what I’ve read so far, I do not see that Swamidass “makes God a monster” in the book. That rather appears to be what comes from Johnson’s hermeneutics, rather than Swamidass’ intentions or expressions. BioLogos was similarly confused, and hadn’t read Kemp, much like Swamidass (that is, until he finally did). Swamidass has previously written about dungeons & suffering, which perhaps by some people may be mistaken as ‘monstrous’. It would be more appropriate and charitable to say, ‘he knows not what he does’ by opening this rift. Thus, he speaks about “what it means to be human?” as a distant (methodological) naturalist, with an important background personal concern involving local fellow YECists and activistic sociology behind the book’s publication (e.g. choice of publishing house).

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Happy New Year

To all TSZ Members and Readers!

The end of the year and the imminent arrival of the new decade made me wonder when exactly Dr Liddle set this blog up. I see it was in (or at least prior to) August, 2011. Lizzie put up her first opening post Where does information come from? here. You can tell it’s the first because the link is to “hello_world”, the example post that comes with the WordPress package. UD addicts may like to follow this link to exchanges between Lizzie and the charming Upright Biped that may have had some part in the birth of TSZ. So TSZ is well on the way to it’s first decade – a remarkable achievement considering Lizzie has not actively participated here for some years.

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Quantum jitters behind DNA mutations

It was just a matter of time before quantum mechanics were to be identified as the driving force behind DNA mutations…

“In the past, we knew DNA polymerases make mistakes during DNA replication but did not know how they do it,” said Zucai Suo, Ph.D., Ohio State professor of chemistry and biochemistry. “Now, our study provides a mechanistic sense for how the mistakes arise.”

The results provide “convincing validation for the chemical origins of mutations proposed by Watson and Crick in 1953,” said Myron Goodman, Ph.D., a professor of molecular biology and chemistry at the University of Southern California, who was not involved in the study. “It is significant scientifically, and even though it took about 65 years to prove, it also demonstrates the folly of ever betting against Watson and Crick.”

One of the surprising discoveries made by the team was that the frequency at which bases shifted their shapes varied with DNA sequence. In one of their experiments, Ohio State biochemists Zucai Suo and Walter Zahurancik essentially counted the number of times that polymerases incorporated the wrong base into the DNA. They found that mistakes were indeed not uniform: they appeared more frequently in some sequences than others. For example, a region with more Gs and Cs might form more quantum jitters, and subsequently more mutations, than an area that was rich in As and Ts.

But, it doesn’t end there…

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How to “cook science”

50% of peer reviewed articles may be not true…How’s that possible? You pay $ and the articles with the results you would like them to be get cooked for you in the most prestigious science journals in the world.

In the video there is also an interesting bit on the cholesterol lowering statins issue in France…Big Pharma demands to put statins in the water…or people will die…

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Of “models” and “algorithms”

I was short with Joe Felsenstein in the comments section of “Stark Incompetence,” a post in which I address, well, um, the stark incompetence on display in a recent publication of Eric Holloway. I have apologized to Joe, and promised to make amends with a brief post on the topic that he wants to address. Now, the topic is a putative model that Eric introduced in “Mutual Algorithmic Information, Information Non-growth, and Allele Frequency” (or perhaps an improved version of the model). Here is a remark that I addressed to Joe:

Tom English: As you know, if a putative model is logically inconsistent, then it is not a model of anything. I claim that that EricMH’s putative model is logically inconsistent. You had better prove that it is consistent, or turn it into something that you can prove is consistent, before going on to discuss its biological relevance.

I will not have to go far into Eric’s post to identify inconsistencies. After explaining the inconsistencies, which I doubt can be eliminated, I will remark on why the “model” is not worth salvaging. The gist is that Eric’s attempted analysis puts a halting, output-generating simulator of a non-halting, non-output-generating evolutionary process in place of the process itself. An analysis of the simulator would not, in any case, be an analysis of the simuland.

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Stark incompetence

David Nemati and Eric Holloway, “Expected Algorithmic Specified Complexity.” Bio-Complexity 2019 (2):1-10. doi:10.5048/BIO-C.2019.2. Editor: William Basener. Editor-in-Chief: Robert J. Marks II.

Let us start by examining a part of the article that everyone can see is horrendous. When I supply proofs, in a future post, that other parts of the article are wrong, few of you will follow the details. But even the mathematically uninclined should understand, after reading what follows, that

  1. the authors of a grotesque mangling of lower-level mathematics are unlikely to get higher-level mathematics correct, and
  2. the reviewers and editors who approved the mangling are unlikely to have given the rest of the article adequate scrutiny.

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Shifting paradigms

Are we beginning to see a major paradigm shift, steadily moving away from the prevailing physicalist, materialist.mechanistic mindset?

Integral theory is one attempt to move beyond any narrow,exclusive views of reality proclaimed by representives of science, religion, philosophy, spiritual traditions or whatever. Jennifer Gidley writes about integral thinking and the evolution of consciousness here

There are periods in human and cultural evolution when humanity passes through such fundamental transformations that our reality shifts and new patterns of thought are required to make sense of the unfolding human drama . . . The profound transformation we are now witnessing has been emerging on a global scale over millennia and has matured to a tipping point and rate of acceleration that has radically altered and will continue to alter our human condition in every aspect. We must therefore expand our perspective and call forth unprecedented narrative powers to name, diagnose, and articulate this shift… Integral philosopher Ashok Gangadean in the opening quotation encapsulates what many integral theorists have been voicing over the past decade. It is this integral research on emergent movement(s) of consciousness that I am referring to as the evolution of consciousness discourse This research points to the emergence of a new structure,stage(s) or movement of consciousness that has been referred to by various terms, most notably, post-formal integral and planetary.

Jude Currivan says that instead of big bang we have the big breath. The “outbreath” that gives rise to the physical unverse. Matter and energy are the products of information. The physical universe is in-formed as she puts it.


She discusses her views here in “Restating and reunifying reality: Our in-formed and holographic universe”.


This is part of an annual Mystics and Scientists conference promoted by The Scientific & Medical Network


The metaphor of the big bang conjures up images of a destructive explosion leading to chaos. But we should imagine the universe as a birth of order and organisation and this is more in keeping with a breathing process by which we communicate compositions of song, poetry and prose. Evolution is the creation of order out of chaos.


So are we seeing a movement to a more integrated, holistic understanding of reality where, rather than being a mere by product of a particular arrangement of matter, consciousness plays a primal, central role? The cosmos is breathed into existence, the out-breathing Word, the Logos, creates the living universe. Consciousness is the alpha and omega.

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Non-conservation of algorithmic specified complexity…

… proved without reference to infinity and the empty string.

Some readers have objected to my simple proof that computable transformation f(x) of a binary string x can result in an infinite increase of algorithmic specified complexity (ASC). Here I give a less-simple proof that there is no upper bound on the difference in ASC of f(x) and x. To put it more correctly, I show that the difference can be any positive real number.

Updated 12/8/2019: The assumptions of my theorem were unnecessarily restrictive. I have relaxed the assumptions, without changing the proof.
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A Conflation of Atheisms

In all the discussions of atheism, I have not yet seen any one make what I take to be a rather simple point: atheism is always relative to a specific conception of God. For this reason, one can be an atheist in one sense and a theist in another. This in turn raises the question whether an atheist is intellectually compelled to investigate every conception of God and refute each of them in order to be entitled to his or her atheism. I want to make a preliminary, crude, and rather obvious distinction between two ways of conceiving of God in order to clarify two distinct kinds of atheism: the mythological conception and the metaphysical conception.

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On how the fear/dread of man upon creatures, given by God after the flood, also manifests itself in creatures fear of each other by bright coloration of their bodies.

After the flood God said the fear/dread of man would be upon all creatures on earth. birds, insects, animals , fishes. this was needed because, seemingly , for the first time man would be intimate with biology and so in danger. thus man had this innate protection. YET how does this work? Is it in the thoughts of creatures?

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Breaking Down Barriers

In the video Moral Technology Conference 2016: Day 1 Lecture 1, NIcanor Perlas advocates participating in global conversations which break down the barriers of compartmentalization.

I share his belief that whoever has the money and power, their vision will be the de facto world we are living in, Those with the power make the prominent worldview, the only worldview that is allowed to be taken seriously. Whether or not it is in keeping with reality it will eventually become reality.

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Evo-Info 4 addendum

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

In “Evo-Info 4: Non-Conservation of Algorithmic Specified Complexity,” I neglected to explain that algorithmic mutual information is essentially a special case of algorithmic specified complexity. This leads immediately to two important points:

  1. Marks et al. claim that algorithmic specified complexity is a measure of meaning. If this is so, then algorithmic mutual information is also a measure of meaning. Yet no one working in the field of information theory has ever regarded it as such. Thus Marks et al. bear the burden of explaining how they have gotten the interpretation of algorithmic mutual information right, and how everyone else has gotten it wrong.
  2. It should not come as a shock that the “law of information conservation (nongrowth)” for algorithmic mutual information, a special case of algorithmic specified complexity, does not hold for algorithmic specified complexity in general.

My formal demonstration of unbounded growth of algorithmic specified complexity (ASC) in data processing also serves to counter the notion that ASC is a measure of meaning. I did not explain this in Evo-Info 4, and will do so here, suppressing as much mathematical detail as I can. You need to know that a binary string is a finite sequence of 0s and 1s, and that the empty (length-zero) string is denoted \lambda. The particular data processing that I considered was erasure: on input of any binary string x, the output \mathtt{erased}(x) is the empty string. I chose erasure because it rather obviously does not make data more meaningful. However, part of the definition of ASC is an assignment of probabilities to all binary strings. The ASC of a binary string is infinite if and only if its probability is zero. If the empty string is assigned probability zero, and all other binary strings are assigned probabilities greater than zero, then the erasure of a nonempty binary string results in an infinite increase in ASC. In simplified notation, the growth in ASC is

    \[A(\mathtt{erased}(x)) - A(x) = \underbrace{A(\lambda)}_\text{infinite} - \underbrace{A(x)}_\text{finite} = \infty\]

for all nonempty binary strings x. Thus Marks et al. are telling us that erasure of data can produce an infinite increase in meaning.

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Number of Unique Commentators

For The Panda’s Thumb’s After the Bar Closes thread on Uncommon Descent, I created a graph of the number of unique commentators at UD:

Here, for each day from Apr 2005 until Nov 2019, I gave the number of different people who commented at UD at least once during the previous 365 days. The colors indicate the number of contributions such a commentator has made over this period of time.

Obviously, the same can be done for “The Skeptical Zone”:

Enjoy!

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The REAL “Problem of Evil”

[moderator’s note: Nonlin.org produced this at about the same time as his “Miracles” post. I delayed this, so that they could be discussed one at a time. I’m now publishing this one.]

[a note to nonlin – if all of your post is one block, it is hard to add a “more” break. Maybe a short introductory sentence as a first block would make that easier]

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